These 3-hour workshops are hands-on, laboratory sessions during which presenters share their innovative and successful undergraduate lab exercises with participants. Participants then review these with short form (pdf) or long form evaluations, part of the peer-review process leading to publication of these activities in our annual Proceedings publication.
Sessions are listed below by day, and you will choose which workshop to attend upon registering for the conference (space is limited).
Wednesday, June 22, 2016
Estimating Fish Population Size using a Mark-Recapture Technique
Ann Cheek
The purpose of this laboratory exercise is to estimate the size of a closed population in the natural environment. The exercise can be completed in 2 laboratory periods. During the first lab period, students capture and mark fish in a local pond. During the second lab period, students capture fish again and calculate an estimate of population size based on the proportion of recaptures they make. In the workshop, participants will label, bait, and set traps. Participants will work in groups of 4 all the Day1 and Day2 activities, including retrieving traps, marking fish at the pond, tallying data, and returning fish safely to the pond. Participants will calculate a population size estimate, then evaluate its validity. The exercise could be used in an Introductory Biology, Ecology, or Ichthyology course, either as a methods exercise or as a guided inquiry activity preparing students to answer their own questions.
Stereoscopic Visualization Using BodyViz and Clinical Embolization of Benign Brain Tumors
Tejendra Gill and Alexandra Ulmet
Clinically induced embolization of benign tumors is a promising procedure which reduces the risk of malignancy. Both physical and chemoembolysis obviate the need for surgery and are the preferred choices depending on the location and accessibility of the tumor. This paper discusses the concept of embolization and its advantages from a clinical perspective. BodyViz, a software which allows stereoscopic visualization of 3D images of CT scans and MRI data, was used in this study to explore images of brain tumor in a patient. Students enrolled in the Human Anatomy & Physiology laboratory and lecture courses at the University of Houston have access to this state-of-the-art diagnostic tool for educational purposes.
Sex in the Garden
Debra Mauzy-Melitz, Hubert Vu, Huong Thien Hguyen
Pollen germination occurs when a pollen grain develops a pollen tube. In nature, pollen germination occurs on the stigma of a flower and the pollen tube elongates towards the flower’s ovule. Pollen germination and elongation is a dynamic process during which pollen must respond to different signals and develop a complex structure to deliver sperm cells for fertilization. Pollen germination can be easily visualized using an in vitro setup and a compound microscope. This system is a simple model to study cell to cell interactions and environmental effects on development. Pollen germination experiments are inexpensive and do not require specialized equipment other than compound microscopes and micropipettors. Multiple laboratory activities have been developed at ICI using pollen germination as the central theme. Students learn about the advantages and disadvantages of different in vitro assay methods, test multiple flower species, modify the basic germination media and design an experiment related to pollen germination. This workshop will allow participants to explore pollen germination and how this system could be used effectively to demonstrate the scientific method and integrate evolution and cell biology.
An Immersion in Vocalizations at the Houston Zoo
Kathleen A. Nolan
Participants in this workshop will travel to the Houston Zoo to record vocalizations of sea lions, birds, and other animals. Audacity is a free-downloadable program that can be used to easily record and analyze animal vocalizations. We will record an animal of interest for approximately a half-hour, and then return to a computer lab to analyze the data. The Audacity file will be opened and the sound tracing recorded will be converted to a spectrogram. Minimum and maximum frequencies will be recorded. Patterns in the vocalizations such as growls, trills, or repetitions such as barks will be recorded and discussed. This very interactive exercise is an example of how to engage students in the study of animals with a wide-range of implications, including behavior and conservation.
Shhhhh…Keep it down! Designing, Making, and Testing shRNA
Alp Oran
This workshop is based on an actual upper-year undergraduate lab course involving RNA interference (RNAi). Specifically, students in this lab learn how to design, make, and test an easily customizable shRNA construct in transfected mammalian cells. For the purposes of this workshop, participants will take part in the beginning and end steps of the course, specifically learning i) how to design and ii) analyze the ‘knock-down’ effect of a shRNA construct targeting enhanced green fluorescent protein (EGFP). Participants will have the chance to learn the basics of shRNA design and engage in activities that mimic the student experiences in the lab. During various intervals, other aspects of the lab course will be explained including how the target gene for knock down can be changed year-after-year to avoid repetition and obsolescence from a teaching and learning standpoint. Strengths and weaknesses will also be shared with the participants based on lab coordinator and student feedback from two different iterations of the course. Suggestions from the audience will also be encouraged.
STEM Technology Applied to Biology Labs: Quantifying Cellular Respiration with Sensors and Arduino Microcontroller Technology
Denise Piechnik, Mary Mulcahy, Brittni Cumberland
Programmable microcontrollers paired with sensors are an easy way to introduce technology into STEM courses. In this workshop, we will show how we converted a traditional cellular respiration lab that relies on indirect measurements of CO2 from pea and yeast respiration, to a more advanced lab that engages students in the use of sensor technology and that provides direct measurements of levels of CO2. Traditional low-tech measurement of CO2 can be inaccurate and frustrating for students and faculty, while direct measurements taken with accurate, pre-fabricated sensors and data loggers are expensive. These pre-fabricated sensing systems promote reliance on a “black box” data logger for data collection, disconnecting students from the measurement and data collection process. We will demonstrate the Arduino, a programmable microcontroller, connected to a digital component CO2 sensor to directly measure CO2 during aerobic and anaerobic respiration. The sensing system that will be demonstrated at the workshop was constructed using lab instrumentation component parts under $200 (not including the laptop or tablet). The Arduino microcontrollers, or the brains of the sensing system, can be reprogrammed and used in many other experiments, including soil moisture sensing and measuring pH. Using the Arduino microcontroller with component sensors requires assembly and some basic programming and electronics skills. Arduinos are popular in the DIY community, so programming and re-programming Arduinos is made easier with support available from a large open source community that freely shares complete sets of code or “sketches” for the Arduino in many applications.
Using herbicides to understand the light-dependent reactions of photosynthesis
Laurel Rodgers and Wendy Peiffer
The electron transport chain (ETC) is a critical part of both photosynthesis and cellular respiration. However, it is frequently one of the topics least understood by our General Biology students. In this lab students first observe the production of oxygen in spinach leaves and the consumption use of carbon dioxide by Elodea leaves during photosynthesis. Next, students perform a skit in which they act out the process of photosynthesis, focusing on the ETC and the light dependent reactions. Finally, students design an experiment that will allow them to determine if a given herbicide blocks the ETC by stealing electrons or by blocking electron movement. This lab increases our students’ basic understanding of photosynthesis and the roll of the ETC in metabolism.
Attack of the Killer Fungus: “Real” Research in the Classroom
Brian Sato
Discovery driven experiments in undergraduate laboratory courses have been shown to increase student learning and critical thinking abilities. This workshop focuses on a lab module involving the nematophagous fungus, Arthrobotrys oligospora, an ecologically relevant organism with potential use as a pest control agent in agricultural settings. A. oligospora is capable of capturing the nematode Caenorhabditis elegans through the formation of circular traps. The goals of this module are to enhance scientific understanding of the regulation of worm capture by soil dwelling fungi and for students to attain a set of established learning goals. Groups of four students are provided with the experimental background and conduct their own literature search to identify a variable that may affect the efficiency of C. elegans capture. Students develop a hypothesis and conduct an experiment to compare worm survival in the control versus variable condition, writing a lab report in the format of a primary research article. From this experimental module, students were able to produce results that agree with published data as well as add to the existing literature, while demonstrating positive gains regarding the learning objectives. Workshop attendees will be introduced to nematophagous fungi, design potential experiments that their students could perform using the established module, and get hands on experience with the organisms and experimental protocol. In addition, we will discuss how to incorporate this module into the lab curriculum at attendees’ institutions along with potential means of assessment to measure student learning.
Authentic Ecology Field Investigation for Large (or small) General Biology Lab Courses
Carolyn Schultz, Ana Strimaitis
This is a two-part community ecology lab that engages students in an authentic field investigation. In part one, students plant pitfall traps for crawling invertebrates in three different habitats. On the day of the planting, students observe biotic and abiotic components of the habitats, discuss community interactions, and predict which organisms might fall into the traps. The following lab meeting, the catch is quantified and specific adaptations that may have benefitted the organism in its habitat are noted and related to natural selection and evolutionary change. Data is depicted in graph format and is compared over many semesters to reveal trends.
Genetic Complementation Testing in C. elegans
Pliny A. Smith
Complementation testing of alleles facilitates genetic identification of phenotypes. The nematode Caenorhabditis elegans rich history of genetic discovery due to its relatively short life cycle, ease of culturing, and a variety of available phenotypes. Many important genetic pathways were first elucidated in C. elegans, and later found to play critical roles in more complex metazoans. This laboratory will apply the technique of genetic complementation of alleles to up to four easy to score phenotypes. After completing the experiment, students analyze their data and present a poster of their results and interpretation of the data to their peers.
Using Gromphadorhina portentosa to study sensory neuron action potentials
Kenneth G. Sossa and Wes Colgan III
Neurophysiological principles are best illustrated using live animal tissue. Here we record Gromphadorhina portentosa leg sensory neuron action potentials using ADInstruments 26T Powerlabs. To begin, G. portentosa were anesthetized at -20°C for about 15 minutes followed by complete excision of a leg. The “Cockroach Sensory Nerve” experiment as outlined in LabTutor by ADInstruments provides easy to follow directions to four exercises. These exercises record and measure sensory neuron action potential intensity (amplitude) and generation (frequency). The first involves testing the effects of different stimuli, e.g. wind. The second exercise examines action potentials among different sensory spines while the third tests how changing the angle of deflection alters the activity. Finally, the fourth investigates the adaptive abilities of sensory spines. Together, these exercises familiarize students with sensory organ functions, key neuroscience concepts, and specialized instrumentation.
Dragon Genetics
Rebecca Williams and Mark Walvoord
Genetics is a topic that most students enjoy but also have trouble understanding. This set of laboratories teaches basic genetics concepts using a fun model, dragons. Groups of students create their own dragon using popsicle sticks as chromosomes, emphasizing the randomness of inheritance. These baby dragons are then used to answer guided question sets to help students learn some of the more difficult introductory genetics concepts. During the second lab students interact with other groups to find a mate for their dragon and to do an activity for understanding test crosses. This lab is based on “Dragon Genetics” by Dr. Pamela Esprivalo Harrell, updated with more reflective prompts to address common student misconceptions.>
Thursday, June 23, 2016
Course-based Research with Bean Beetles, Collosobruchus maculatus, and a Y-maze Olfactometer
Lawrence Blumer and Ronald Ty Smith
Course-based authentic research is an effective and appropriate substitute for mentored research with undergraduates to both engage students in the process of science and to foster the skills and knowledge development required to successfully pursue advanced studies. Here we describe a very flexible olfactometery system that can be used for a wide range of open-ended experimental studies using the bean beetle, Callosobruchus maculatus, model organism. The essence of this olfactometer is a Y-maze in which individual beetles choose between two sources of chemical signals. We will use this system to address questions about mate choice by males in this species. This system may be used with a guided inquiry pedagogy to start a process that leads to students posing their own questions and pursuing authentic research projects.
Estimating Fish Population Size using a Mark-Recapture Technique
Ann Cheek
The purpose of this laboratory exercise is to estimate the size of a closed population in the natural environment. The exercise can be completed in 2 laboratory periods. During the first lab period, students capture and mark fish in a local pond. During the second lab period, students capture fish again and calculate an estimate of population size based on the proportion of recaptures they make. In the workshop, participants will label, bait, and set traps. Participants will work in groups of 4 all the Day1 and Day2 activities, including retrieving traps, marking fish at the pond, tallying data, and returning fish safely to the pond. Participants will calculate a population size estimate, then evaluate its validity. The exercise could be used in an Introductory Biology, Ecology, or Ichthyology course, either as a methods exercise or as a guided inquiry activity preparing students to answer their own questions.
Identification of Unknown Fluorescent Proteins: A Colorful Lab Module for Teaching Gene-to-Protein Information Flow and Protein Structure
Aaron Coleman
Fluorescent proteins impart specific colors to coelenterate marine organisms such as jellyfish and corals. Green fluorescent protein (GFP; from the jellyfish Aequorea victoria) and DsRed (from the coral Discosoma sp) have been adapted for use as fluorescent tags for the real-time imaging of proteins in living cells, leading to a revolution in cell biology research. These proteins also make fun and engaging tools for teaching biology and biochemistry. Here we describe a lab module in which students identify unknown fluorescent proteins by performing spectrophotometry and SDS-PAGE. Students are assigned an unknown gene from a panel of 12 cDNAs encoding various fluorescent proteins derived from GFP or DsRed. These fluorescent proteins differ in their fluorescence properties and subunit composition. The students receive the genes in a bacterial expression vector and proceed to express the fluorescent proteins in E. coli, followed by rapid purification via a poly-histidine tag added by the vector. Three pieces of evidence allow for identification of the unknown. The color of the bacterial colonies allows students to determine if their protein is a derivative of GFP or DsRed. The absorption spectrum of the fluorescent protein is measured on a spectrophotometer, allowing unknowns from the same parent protein to be identified by their excitation max. Some of the unknowns, however, have excitation maximums that are identical or too close to determine. These can only be distinguished by determining their subunit composition through running heated (denatures complexes) and unheated (complexes remain intact) samples on SDS-PAGE and analyzing the banding pattern of the stained gel. Correctly interpreting the gel requires students to understand how different length polypeptides are encoded on the gene, how these come together to form a dimer or tetramer, and how these would run under native and denaturing conditions.
Developing collaborative lab experiments across disciplines through the identification of bacteria
Brian Forster
Objectives outlined in Science for All Americans (SAA) include that students will be exposed to science as a collaborative effort. Collaboration allows scientists to learn from one another and work together to answer questions. SAA also states that there should be an emphasis that science is a collection of different scientific fields or content disciplines. Teaching within the laboratory should be consistent with the nature of scientific inquiry. To this end, our university has developed a framework for collaboration between lab classes with a central theme of non-science majors identifying bacteria. We developed a 4-week collaborative laboratory exercise in which non-science majors from a general biology course are grouped with non-science majors in an environmental science course. Prior to the start of the lab activity, students from both courses work with bacteria. Biology students learn about cellular and biochemical characteristics while environmental students learn how to detect bacteria in water. These groups are presented with a sample of water and are tasked with identifying any bacteria that is present in the water. The water that was given to each group was previously inoculated with known bacterial strains by the instructors. Since there are limited directions in the student handout, group members must rely on one another and the knowledge they bring to the group in order to complete the assignment. In Spring 2015, this experiment was performed by students taking either biology or environmental science. Each group was successful in identifying the bacteria in their water. We suggest that such an activity allows students to be exposed to the concept of collaboration in the scientific community with the goal of addressing a single problem. In this workshop, participants will go through the lab activity to identify bacteria present in a water sample and will learn how to develop their own collaborative lab activities between classes.
Collaboration Between Educators and Deep Ocean Scientists to Create Research-Based Labs: Focus on Bioinformatics
Angela Gee
A collaborative team involved with the Center for Dark Energy Biosphere Investigations (CDEBI) funded by the National Science Foundation created a resource of teaching tools for community college instructors. C-DEBI is a group of institutions doing groundbreaking research on the deep ocean biosphere. Scientists, instructors, educators and multimedia designers have collaboratively developed and implemented ways to bring this research to curricula in the sciences. Toolkits were created which are stand-alone labs and activities that can be integrated into relevant curriculum. All materials are open source and posted at http://www.coexploration.org/C-DEBI. Toolkits cover a range of topics for a variety of courses. For this workshop, the focus will be on one toolkit addressing bioinformatics for biology courses which can be modified for physiology, evolution, genomics and molecular and cell biology. The lab is entitled “Amino acid sequence analysis of cytochrome C in bacteria and
Eukarya using bioinformatics.” The objective is for students to understand and use bioinformatics with the programs BLAST and Seaview. Students will compare and contrast amino acid sequences of cytochrome C in humans, other animals and bacteria to investigate genome evolution and protein function. Bioinformatics is a valuable, well-used tool by scientists so it is critical that students are exposed to this technique. After, a discussion on how to adapt this lab to specific curriculum will occur. Then a brief overview of other lab activities available will be presented such as hydrothermal vents for marine science and deep-sea microbes for microbiology. This lab demonstration will showcase how cutting-edge research of C-DEBI can be bought directly to the community college classroom as well as high school and university courses.
Examining microbial biodiversity in soil: A research-based introductory laboratory course.
Stephanie Mel and Stanley Lo
Discussions on biodiversity in introductory courses often focus on taxonomic characterization of macroscopic organisms and their evolutionary relationships. Students may not be aware that most species on earth, especially microbial species, have yet to be identified. Here, we describe a 10-week introductory biology laboratory course focused on microbial biodiversity. The course is designed as an independent, on-going research program, and students are the primary researchers contributing novel data to the project. The goal of this course is to help students develop an understanding for research in biology through inquiry-based laboratory experiments. Students work in teams to collect, analyze, and present original research data while learning core biology concepts and laboratory methods common to a variety of disciplines. Specifically, we are examining if and how microbial communities in soil are different underneath native vs. invasive plant species in a Southern California diversity hotspot. Students analyze soil properties such as moisture and pH and correlate them to functional and genetic biodiversity of the microbial communities. Together, these elements span across the macroscopic and molecular scales in biology, providing opportunities for students to connect their learning across different biology disciplines.
Microrespirometers, mealworms, and mini-lab reports: observing respiration in real-time using a low-tech device
Kevin Miller
Cellular respiration and other biochemical cellular processes can be a difficult topics for students to understand. Having hands-on laboratory activities that cover difficult concepts can help to solidify learning of those concepts. This major workshop will revisit a topic presented in a mini-workshop at last year’s ABLE meeting at Boston University involving the use of microrespirometers to measure the difference in respiration of the mealworm Tenebrio molitor (Coleoptera: Tenebrionidae) at different temperatures. This will be done in an effort to provide greater detail of the device, time for discussion about the laboratory exercise, and a suggestion on how to present findings from the exercise using a mini-lab report format.
Engaging Students in Informed Design Case Studies that Reinforce Laboratory Content
Brian Shmaefsky
This pedagogical strategy demonstrated in this workshop models the Vision and Change in Undergraduate Biology Education (AAAS and NSF) recommendations to highlight new and existing resources for effecting change in college biology teaching. The project used student-centered-authentic applied research investigations to reinforce laboratory content. Groups of college students worked together on scenarios in which they had to apply biology laboratory content for designing a sustainable way of resolving a social need. In one scenario, student teams were asked to design a simple to use and low-cost water toxicology test using local resources in a developing nation. Pre-test and post-test assessments on experimental and control groups showed that students involved in the project performed significantly better on the two student learning outcomes targeted for the study. Student satisfaction surveys indicated that the high school students exited with better attitudes about biology college-level coursework. The use of the informed-design approach in laboratory teaching produces the following outcomes:
- Engage students as active participants, giving them greater control over the learning process.
- Assist students to integrate learning from language, the arts, mathematics, and science laboratory knowledge.
- Encourage pluralistic thinking, avoiding a right/wrong dichotomy and suggesting instead that multiple solutions are possible.
- Provide students an opportunity to reflect upon, revise, and extend their internal models of the world.
- Encourage student to put themselves in the minds of others as they think about how their designs will be understood and used.
Participants in the workshop will divide into groups and be given scenarios to develop a reliable test for investigating water toxicity. Each scenario must be resolved using materials provided to the groups.
Fish Models for Testing Guppy Mate Choice
John Stewart, Donald French, Michael Moore, and Lance Forshee
A study of proximate causation of mate choice can be to engage students in the topic of sexual selection. We developed a new and flexible method for observing mate choice behavior in guppies (Poecilia reticulata.) Students observe male preference for 3D-printed fish models of female fish of different sizes, colors, and shapes to better understand what traits are important in sexual selection. In their first week of the investigation, the students expose a male guppy to a standard suite of different 3D-printed models. They then request modifications for the next week and the week afterward. The investigation engages students’ abilities to carefully observe animals, quantify those observations, and use evolutionary reasoning to communicate their findings in a scientific manuscript peer-reviewed by anonymous new scientists. The use of 3-D printers overcomes a hurdle (crafting accurate models that can be manipulated) making this type of authentic research accessible to a large and broader audience.
Dragon Genetics
Rebecca Williams and Mark Walvoord
Genetics is a topic that most students enjoy but also have trouble understanding. This set of laboratories teaches basic genetics concepts using a fun model, dragons. Groups of students create their own dragon using popsicle sticks as chromosomes, emphasizing the randomness of inheritance. These baby dragons are then used to answer guided question sets to help students learn some of the more difficult introductory genetics concepts. During the second lab students interact with other groups to find a mate for their dragon and to do an activity for understanding test crosses. This lab is based on “Dragon Genetics” by Dr. Pamela Esprivalo Harrell, updated with more reflective prompts to address common student misconceptions.